Multiple sequence alignment - TraesCS6A01G291700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G291700 chr6A 100.000 2323 0 0 1 2323 523644910 523642588 0.000000e+00 4290
1 TraesCS6A01G291700 chr6A 94.656 973 39 4 1353 2323 200490170 200489209 0.000000e+00 1496
2 TraesCS6A01G291700 chr2A 95.478 973 41 3 1353 2323 504224717 504225688 0.000000e+00 1550
3 TraesCS6A01G291700 chr2A 94.564 975 49 3 1353 2323 579388662 579389636 0.000000e+00 1504
4 TraesCS6A01G291700 chr2A 97.120 382 9 2 965 1344 724271982 724272363 0.000000e+00 643
5 TraesCS6A01G291700 chr4D 95.119 963 45 1 1 963 65600750 65599790 0.000000e+00 1517
6 TraesCS6A01G291700 chr5A 94.867 974 43 5 1353 2323 12607751 12606782 0.000000e+00 1515
7 TraesCS6A01G291700 chr1A 94.845 970 46 3 1355 2323 205391358 205392324 0.000000e+00 1511
8 TraesCS6A01G291700 chr1A 94.656 973 50 2 1353 2323 206412819 206413791 0.000000e+00 1507
9 TraesCS6A01G291700 chr1A 98.201 389 6 1 965 1352 554472460 554472072 0.000000e+00 678
10 TraesCS6A01G291700 chr3A 94.742 970 49 2 1356 2323 338489524 338490493 0.000000e+00 1507
11 TraesCS6A01G291700 chr1D 94.928 966 44 2 1 963 331765140 331764177 0.000000e+00 1507
12 TraesCS6A01G291700 chr1D 97.120 382 9 2 965 1344 254483115 254483496 0.000000e+00 643
13 TraesCS6A01G291700 chr7D 94.824 966 45 2 1 963 390102955 390101992 0.000000e+00 1502
14 TraesCS6A01G291700 chr7D 94.542 971 46 5 1 970 508586473 508585509 0.000000e+00 1493
15 TraesCS6A01G291700 chr6D 94.824 966 45 2 1 963 337171889 337172852 0.000000e+00 1502
16 TraesCS6A01G291700 chr3D 94.824 966 45 2 1 963 530110455 530111418 0.000000e+00 1502
17 TraesCS6A01G291700 chr2D 94.824 966 45 2 1 963 303727343 303728306 0.000000e+00 1502
18 TraesCS6A01G291700 chr2D 98.201 389 6 1 965 1352 628290378 628289990 0.000000e+00 678
19 TraesCS6A01G291700 chr2D 97.906 382 6 2 965 1344 628289845 628289464 0.000000e+00 660
20 TraesCS6A01G291700 chr2D 97.382 382 8 2 965 1344 643859479 643859860 0.000000e+00 649
21 TraesCS6A01G291700 chr5D 94.808 963 48 1 1 963 243973478 243972518 0.000000e+00 1500
22 TraesCS6A01G291700 chr5D 94.819 965 45 2 1 962 444803647 444804609 0.000000e+00 1500
23 TraesCS6A01G291700 chr5D 97.906 382 6 2 965 1344 483801638 483801257 0.000000e+00 660
24 TraesCS6A01G291700 chr5D 96.335 382 11 3 965 1344 6218063 6217683 1.960000e-175 625
25 TraesCS6A01G291700 chr7A 94.536 970 49 4 1357 2323 342433023 342433991 0.000000e+00 1495
26 TraesCS6A01G291700 chr7A 94.450 973 47 3 1353 2323 156171810 156170843 0.000000e+00 1491
27 TraesCS6A01G291700 chr3B 97.943 389 7 1 965 1352 201499676 201500064 0.000000e+00 673


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G291700 chr6A 523642588 523644910 2322 True 4290 4290 100.0000 1 2323 1 chr6A.!!$R2 2322
1 TraesCS6A01G291700 chr6A 200489209 200490170 961 True 1496 1496 94.6560 1353 2323 1 chr6A.!!$R1 970
2 TraesCS6A01G291700 chr2A 504224717 504225688 971 False 1550 1550 95.4780 1353 2323 1 chr2A.!!$F1 970
3 TraesCS6A01G291700 chr2A 579388662 579389636 974 False 1504 1504 94.5640 1353 2323 1 chr2A.!!$F2 970
4 TraesCS6A01G291700 chr4D 65599790 65600750 960 True 1517 1517 95.1190 1 963 1 chr4D.!!$R1 962
5 TraesCS6A01G291700 chr5A 12606782 12607751 969 True 1515 1515 94.8670 1353 2323 1 chr5A.!!$R1 970
6 TraesCS6A01G291700 chr1A 205391358 205392324 966 False 1511 1511 94.8450 1355 2323 1 chr1A.!!$F1 968
7 TraesCS6A01G291700 chr1A 206412819 206413791 972 False 1507 1507 94.6560 1353 2323 1 chr1A.!!$F2 970
8 TraesCS6A01G291700 chr3A 338489524 338490493 969 False 1507 1507 94.7420 1356 2323 1 chr3A.!!$F1 967
9 TraesCS6A01G291700 chr1D 331764177 331765140 963 True 1507 1507 94.9280 1 963 1 chr1D.!!$R1 962
10 TraesCS6A01G291700 chr7D 390101992 390102955 963 True 1502 1502 94.8240 1 963 1 chr7D.!!$R1 962
11 TraesCS6A01G291700 chr7D 508585509 508586473 964 True 1493 1493 94.5420 1 970 1 chr7D.!!$R2 969
12 TraesCS6A01G291700 chr6D 337171889 337172852 963 False 1502 1502 94.8240 1 963 1 chr6D.!!$F1 962
13 TraesCS6A01G291700 chr3D 530110455 530111418 963 False 1502 1502 94.8240 1 963 1 chr3D.!!$F1 962
14 TraesCS6A01G291700 chr2D 303727343 303728306 963 False 1502 1502 94.8240 1 963 1 chr2D.!!$F1 962
15 TraesCS6A01G291700 chr2D 628289464 628290378 914 True 669 678 98.0535 965 1352 2 chr2D.!!$R1 387
16 TraesCS6A01G291700 chr5D 243972518 243973478 960 True 1500 1500 94.8080 1 963 1 chr5D.!!$R2 962
17 TraesCS6A01G291700 chr5D 444803647 444804609 962 False 1500 1500 94.8190 1 962 1 chr5D.!!$F1 961
18 TraesCS6A01G291700 chr7A 342433023 342433991 968 False 1495 1495 94.5360 1357 2323 1 chr7A.!!$F1 966
19 TraesCS6A01G291700 chr7A 156170843 156171810 967 True 1491 1491 94.4500 1353 2323 1 chr7A.!!$R1 970

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
88 89 1.228769 TCCGAGTAGGTGGCAGTGT 60.229 57.895 0.0 0.0 41.99 3.55 F
613 614 1.432514 CAGAGACCACAATGACACGG 58.567 55.000 0.0 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1053 1057 1.740025 CCAAAGATTTCGGTCAGAGCC 59.260 52.381 0.00 0.00 0.00 4.70 R
2116 2219 2.122768 AGGCCATGTTTGGTTCCAAAA 58.877 42.857 17.04 9.28 45.57 2.44 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 1.228769 TCCGAGTAGGTGGCAGTGT 60.229 57.895 0.00 0.00 41.99 3.55
111 112 2.099263 GTCGCTCATGCTGGTTCTACTA 59.901 50.000 0.00 0.00 36.97 1.82
143 144 7.817962 TCAAGTGGACTAGTTGCTTAGTTTATC 59.182 37.037 0.00 0.00 39.17 1.75
157 158 6.128254 GCTTAGTTTATCTTCAAGGGTGTGTC 60.128 42.308 0.00 0.00 0.00 3.67
275 276 6.041182 TGTTCTTCTTGCAGTTGGTACTACTA 59.959 38.462 0.00 0.00 31.96 1.82
296 297 6.054295 ACTACTCGTATCTTCGTGTTCCTAT 58.946 40.000 0.00 0.00 38.27 2.57
420 421 2.092212 CCCTTCTAGCCATCCATGTTGT 60.092 50.000 0.00 0.00 0.00 3.32
482 483 2.107366 TCAGATTGCAGGATCCACGTA 58.893 47.619 15.82 0.60 0.00 3.57
613 614 1.432514 CAGAGACCACAATGACACGG 58.567 55.000 0.00 0.00 0.00 4.94
616 617 2.832129 AGAGACCACAATGACACGGTAT 59.168 45.455 0.00 0.00 0.00 2.73
625 626 4.261801 CAATGACACGGTATTTCCTCCTT 58.738 43.478 0.00 0.00 0.00 3.36
637 638 4.451150 CTCCTTGCCGGCGTGCTA 62.451 66.667 23.90 0.00 0.00 3.49
792 793 4.776322 CACAGGGATGGCGGCGAA 62.776 66.667 12.98 0.00 0.00 4.70
808 809 1.971167 GAAACAGCGGTGATGGGCA 60.971 57.895 23.44 0.00 0.00 5.36
865 869 2.109387 AACGGCGGCGGCATATTA 59.891 55.556 35.05 0.00 42.47 0.98
875 879 1.531149 GCGGCATATTAATGAGTGCGT 59.469 47.619 12.92 0.00 38.43 5.24
898 902 5.298527 GTGTGTGGGAGCTTACTTTAGTTTT 59.701 40.000 0.00 0.00 0.00 2.43
899 903 6.484308 GTGTGTGGGAGCTTACTTTAGTTTTA 59.516 38.462 0.00 0.00 0.00 1.52
963 967 9.219497 CTAGTACACGTAAACATTAGACTTAGC 57.781 37.037 0.00 0.00 0.00 3.09
1185 1189 2.233922 AGCCTGTGTACAAGCTCGTAAT 59.766 45.455 9.81 0.00 39.25 1.89
1201 1205 1.261619 GTAATGAAGGGCGCGATCTTG 59.738 52.381 12.10 0.00 0.00 3.02
1235 1240 3.872696 TGAAATTATCCGAGCAGCTTGA 58.127 40.909 11.73 4.60 0.00 3.02
1379 1384 7.691050 CAGCGCTTTTATTAGTTAGTACCAAAC 59.309 37.037 7.50 1.35 0.00 2.93
1612 1710 4.155709 TGGATTTGGATGTTTTAGGTGCA 58.844 39.130 0.00 0.00 0.00 4.57
1782 1883 5.530712 CATGAGTGAGACATAGACAGATGG 58.469 45.833 0.00 0.00 0.00 3.51
2021 2123 1.268625 GTTTTAAGTTGGGGTGGAGCG 59.731 52.381 0.00 0.00 0.00 5.03
2116 2219 8.504005 CATTTCGACTTATAAGTTGGTGACTTT 58.496 33.333 25.99 7.78 46.34 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.032657 TCCTCTTCCTCTTCGCCGAG 61.033 60.000 0.00 0.00 0.00 4.63
143 144 0.532862 AGCACGACACACCCTTGAAG 60.533 55.000 0.00 0.00 0.00 3.02
157 158 3.376935 CTACTGGGGCCTCAGCACG 62.377 68.421 33.33 16.92 46.55 5.34
242 243 6.428159 CCAACTGCAAGAAGAACAGTAGTAAT 59.572 38.462 0.00 0.00 43.63 1.89
275 276 5.125097 ACAATAGGAACACGAAGATACGAGT 59.875 40.000 0.00 0.00 38.52 4.18
420 421 3.056179 TGACTCATGTGAGCCGTTTGATA 60.056 43.478 9.84 0.00 45.79 2.15
482 483 1.625818 ACCTTCGAGACCTTGAATGCT 59.374 47.619 0.54 0.00 32.91 3.79
593 594 1.432514 CGTGTCATTGTGGTCTCTGG 58.567 55.000 0.00 0.00 0.00 3.86
595 596 1.048601 ACCGTGTCATTGTGGTCTCT 58.951 50.000 0.00 0.00 0.00 3.10
601 602 3.374058 GGAGGAAATACCGTGTCATTGTG 59.626 47.826 0.00 0.00 44.74 3.33
613 614 1.436983 CGCCGGCAAGGAGGAAATAC 61.437 60.000 28.98 0.00 45.00 1.89
616 617 3.948719 ACGCCGGCAAGGAGGAAA 61.949 61.111 28.98 0.00 44.78 3.13
712 713 4.498520 CTCGTGATGCCTCCGCGT 62.499 66.667 4.92 0.00 38.51 6.01
718 719 2.060980 GTCCCTCCTCGTGATGCCT 61.061 63.158 0.00 0.00 0.00 4.75
792 793 1.973281 CTTGCCCATCACCGCTGTT 60.973 57.895 0.00 0.00 0.00 3.16
808 809 0.603065 GCTCCGGCCAACAATTTCTT 59.397 50.000 2.24 0.00 0.00 2.52
865 869 0.603707 CTCCCACACACGCACTCATT 60.604 55.000 0.00 0.00 0.00 2.57
875 879 4.699925 AACTAAAGTAAGCTCCCACACA 57.300 40.909 0.00 0.00 0.00 3.72
963 967 0.996462 TGAAAAAGATACCGCGAGCG 59.004 50.000 8.23 10.86 39.44 5.03
1053 1057 1.740025 CCAAAGATTTCGGTCAGAGCC 59.260 52.381 0.00 0.00 0.00 4.70
1142 1146 5.833082 CTTCTAAAGCCACTCGATTAGCTA 58.167 41.667 0.00 0.00 34.49 3.32
1185 1189 2.819595 GCAAGATCGCGCCCTTCA 60.820 61.111 0.00 0.00 0.00 3.02
1201 1205 5.452777 GGATAATTTCATTACCTTGCGAGC 58.547 41.667 0.00 0.00 0.00 5.03
1235 1240 3.619979 CGGCTAGTTCAGGACTCCATTTT 60.620 47.826 0.00 0.00 39.86 1.82
1782 1883 7.084486 TCTCTCATGTATACACAATGTATCGC 58.916 38.462 7.96 1.73 42.16 4.58
1979 2081 8.999905 AAACTTATAAGTGACCCCTTTTTACA 57.000 30.769 18.70 0.00 39.66 2.41
2116 2219 2.122768 AGGCCATGTTTGGTTCCAAAA 58.877 42.857 17.04 9.28 45.57 2.44


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.